Preprints
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges
SM Cavany, C Barbera, M Carpenter, C Rodgers, M Stenglein, C Mayo, TA Perkins
bioRxiv doi:10.1101/2022.06.03.494504
html | pdf
Expected endpoints from future chikungunya vaccine trial sites informed by serological data and modeling
QM Tran, KJ Soda, AS Siraj, SM Moore, HE Clapham, TA Perkins
medRxiv doi:10.1101/2022.05.23.22275466
html | pdf | code
Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
ML Poterek, CBF Vogels, ND Grubaugh, GD Ebel, TA Perkins, SM Cavany
medRxiv doi:10.1101/2022.05.05.22274743
html | pdf
An epidemiological and intervention assessment of the malaria epidemic in Bolivar, Venezuela: a modelling study
JH Huber, LF Chaves, AS Siraj, JE Moreno, ME Guevara, M Villegas, L Pocaterra, L Villegas, TA Perkins
medRxiv doi:10.1101/2022.04.19.22274042
html | pdf
Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study
RK Borchering, LC Mulllany, E Howerton, M Chinazzi, CP Smith, M Qin, NG Reich, L Contamin, J Levander, J Kerr, J Espino, H Hochheiser, K Lovett, M Kinsey, K Tallaksen, S Wilson, L Shin, JC Lemaitre, JD Hulse, J Kaminsky, EC Lee, JT Davis, K Mu, X Xiong, A Pastore y Piontti, A Vespignani, A Srivastava, P Porebski, S Venkatramanan, A Adiga, B Lewis, B Klahn, J Outten, B Hurt, J Chen, H Mortveit, A Wilson, M Marathe, S Hoops, P Bhattacharya, D Machi, S Chen, R Paul, D Janies, JC Thill, M Galanti, T Yamana, S Pei, J Shaman, G España, S Cavany, S Moore, TA Perkins, JM Healy, RB Slayton, MA Johansson, M Biggerstaff, K Shea, SA Truelove, MC Runge, C Viboud, J Lessler
medRxiv doi:10.1101/2022.03.08.22271905
html | pdf
Prioritizing interventions for preventing COVID-19 outbreaks in military basic training
G España*, TA Perkins*, S Pollett, ME Smith, SM Moore, PO Kwon, TL Hall, MH Beagle Jr., CK Murray, S Hakre, S Peel, K Modjarrad, PT Scott
medRxiv doi:10.1101/2021.11.28.21266969
html | pdf | code
Ignoring transmission dynamics leads to underestimation of the impact of a novel intervention against mosquito-borne disease
SM Cavany*, JH Huber*, A Wieler, M Elliott, QM Tran, G España, SM Moore, TA Perkins
medRxiv doi:10.1101/2021.11.19.21266602
html | pdf
Misdiagnosis prevents accurate monitoring of transmission and burden for sub-critical pathogens: a case study of Plasmodium knowlesi malaria
JH Huber
medRxiv doi:10.1101/2021.09.13.21263501
html | pdf
The potential impact of delta variant of SARS-CoV-2 in the context of limited vaccination coverage and increasing social mixing in Bogotá, Colombia
G España, ZM Cucunubá, J Cuervo-Rojas, H Díaz, M González-Mayorga, JD Ramírez
medRxiv doi:10.1101/2021.08.06.21261734
html | pdf
COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support
K Shea, RK Borchering, WJM Probert, E Howerton, TL Bogich, S Li, WG van Panhuis, C Viboud, R Aguas, A Belov, SH Bhargava, S Cavany, JC Chang, C Chen, J Chen, S Chen, YQ Chen, LM Childs, CC Chow, I Crooker, SY Del Valle, G España, G Fairchild, RC Gerkin, TC Germann, Q Gu, X Guan, L Guo, GR Hart, TJ Hladish, N Hupert, D Janies, CC Kerr, DJ Klein, E Klein, G Lin, C Manore, LA Meyers, J Mittler, K Mu, RC Nunez, R Oidtman, R Pasco, A Pastore y Pionti, R Paul, CAB Pearson, D Perdomo, TA Perkins, K Pierce, AN Pillai, RC Rael, K Rosenfeld, CW Ross, JA Spencer, AB Stoltzfus, KB Toh, S Vattikuti, A Vespignani, L Wang, L White, P Xu, Y Yang, ON Yogurtcu, W Zhang, Y Zhao, D Zou, M Ferrari, D Pannell, M Tildesley, J Seifarth, E Johnson, M Biggerstaff, M Johansson, RB Slayton, J Levander, J Stazer, J Salermo, MC Runge
medRxiv doi:10.1101/2020.11.03.20225409
html | pdf
Ensemble forecasts of coronavirus disease 2019 (COVID-19) in the U.S.
EL Ray, N Wattanachit, J Niemi, AH Kanji, K House, EY Cramer, J Bracher, Andrew Zheng, TK Yamana, X Xiong, S Woody, Y Wang, L Wang, RL Walraven, V Tomar, K Sherratt, D Sheldon, RC Reiner, BA Prakash, D Osthus, ML Li, EC Lee, U Koyluoglu, P Keskinocak, Y Gu, Q Gu, GE George, G España, S Corsetti, J Chhatwal, S Cavany, H Biegel, M Ben-Nun, J Walker, R Slayton, V Lopez, M Biggerstaff, MA Johansson, NG Reich, COVID-19 Forecast Hub Consortium
medRxiv doi:10.1101/2020.08.19.20177493
html | pdf
2022
The impact of emerging Plasodium knowlesi on accurate diagnosis by light microscopy: a systematic review and modeling analysis
JH Huber, M Elliott, C Koepfli, TA Perkins
In press at American Journal of Tropical Medicine and Hygiene
html | pdf
Designing school reopening in the COVID-19 pre-vaccination period in Bogotá, Colombia: A modeling study
G España*, Z Cucunubá*, H Diaz, S Cavany, N Castañeda, L Rodriguez
PLOS Global Public Health 2:e0000467
html | pdf
Projecting vaccine demand and impact for emerging zoonotic pathogens
A Lerch, QA ten Bosch, M L'Azou-Jackson, AA Bettis, M Bernuzzi, GAV Murphy, QM Tran, JH Huber, A Siraj, M Elliott, C Hartlage, K Koh, K Strimbu, M Walters, TA Perkins, SM Moore
BMC Medicine
html | pdf | code | app
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States
EY Cramer, EL Ray, VK Lopez, ... , 284 authors including S Cavany, G España, S Moore, R Oidtman, TA Perkins, ... , RB Slayton, MA Johansson, M Biggerstaff, NG Reich
Proceedings of the National Academy of Sciences 119:e2113561119
html | pdf
Inferring person-to-person networks of pathogen transmission: is routine surveillance data up to the task?
JH Huber, MS Hsiang, N Dlamini, M Murphy, S Vilakati, N Nhlabathi, A Lerch, R Nielsen, N Ntshalintshali, B Greenhouse, TA Perkins
Malaria Journal 21:58
html | pdf
Bluetongue research at a crossroads: modern genomics tools can pave the way to new insights
J Kopanke, M Carpenter, J Lee, K Reed, C Rodgers, M Burton, K Lovett, JA Westrich, E McNulty, E McDermott, C Barbera, S Cavany, JR Rohr, TA Perkins, CK Mathiason, M Stenglein, C Mayo
Annual Review of Animal Biosciences 10:303
html | pdf
Performance of three molecular tests for SARS-CoV-2 on a university campus estimated jointly with Bayesian latent class modeling
TA Perkins, M Stephens, W Alvarez Barrios, SM Cavany, L Rulli, ME Pfrender
Microbiology Spectrum
html | pdf | code
Inferring SARS-CoV-2 RNA shedding into wastewater relative to time of infection
SM Cavany, A Bivins, Z Wu, D North, K Bibby*, TA Perkins*
Epidemiology and Infection
html | pdf
2021
Site-specific biases in phase-III clinical trials underestimate the effect of radical cure against Plasmodium vivax hypnozoites
JH Huber, C Koepfli, G España, N Nekkab, MT White, TA Perkins
Malaria Journal
html | pdf
Timing is everything when it comes to pertussis vaccination
TA Perkins, QM Tran
Lancet Infectious Diseases
html
The current burden of Japanese encephalitis and the estimated impacts of vaccination: Combining estimates of the spatial distribution and transmission intensity of a zoonotic pathogen
SM Moore
PLOS Neglected Tropical Diseases 15:e0009385
html | pdf | code
Burden is in the eye of the beholder: sensitivity of yellow fever disease burden estimates to modeling assumptions
TA Perkins, JH Huber, QM Tran, RJ Oidtman, MK Walters, AS Siraj, SM Moore
Science Advances 7:eabg5033
html | pdf | code
Trade-offs between individual and ensemble forecasts of an emerging infectious disease
RJ Oidtman, E Omodei, MUG Kraemer, CA Castaneda-Orjuela, E Cruz-Rivera, S Misnaza-Castrillon, MP Cifuentes, LE Rincon, V Canon, P de Alarcon, G España, JH Huber, SC Hill, CM Barker, MA Johansson, CA Manore, RC Reiner, I Rodriguez-Barraquer, AS Siraj, E Frias-Martinez, M Garcia-Herranz, TA Perkins
Nature Communications 12:5379
html | pdf
Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA
G España, SM Cavany*, RJ Oidtman*, C Barbera, A Costello, A Lerch, M Poterek, Q Tran, A Wieler, S Moore, TA Perkins
Epidemics 37:100487
html | pdf
Pre-preprint: August 21, 2020
Initial Twitter thread: August 21, 2020
Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world
J Toor, S Echeverria-Londono, X Li, K Abbas, ED Carter, HE Clapham, A Clark, MJ de Villiers, K Eilertson, M Ferrari, I Gamkrelidze, TB Hallett, WR Hinsley, D Hogan, JH Huber, ML Jackson, K Jean, M Jit, A Karachaliou, P Klepac, A Kraay, J Lessler, X Li, BA Lopman, T Mengistu, CJE Metcalf, SM Moore, S Nayagam, T Papadopoulos, TA Perkins, A Portnoy, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, Y Tam, H Tanvir, QM Tran, CL Trotter, SA Truelove, E Vynnycky, N Walker, A Winter, K Woodruff, NM Ferguson, KAM Gaythorpe
eLife 10:e67635
html | pdf
The impact of dengue illness on social distancing and caregiving behavior
KL Schaber, AC Morrison, WH Elson, H Astete-Vega, JJ Córdova-López, EJ Ríos López, WL Quiroz Flores, AS Vizcarra Santillan, TW Scott, LA Waller, U Kitron, CM Barker, TA Perkins, AL Rothman, G Vazquez-Prokopec, JP Elder
PLOS Neglected Tropical Diseases
html | pdf
Cost-effectiveness of dengue vaccination in Puerto Rico
G España, AJ Leidner, S Waterman, TA Perkins
PLOS Neglected Tropical Diseases
html | pdf
Pandemic-associated mobility restrictions could cause increases in dengue virus transmission
SM Cavany, G España, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases
html | pdf
Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries
K Gaythorpe*, K Abbas*, JH Huber*, A Karachaliou*, N Thakkar*, K Woodruff, X Li, S Echeverria-Londono, VIMC Working Group on COVID-19 Impact on Vaccine Preventable Disease, M Ferrari^, ML Jackson^, K McCarthy^, TA Perkins^, C Trotter^, M Jit^
eLife 10:e67023
html | pdf
Over 100 years of Rift Valley fever: a patchwork of data on pathogen spread and spillover
GM Bron, K Strimbu, H Cecilia, A Lerch, SM Moore, Q Tran, TA Perkins, QA ten Bosch
Pathogens 10:708
html | pdf
Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
AF Brito*, LC Machado*, RJ Oidtman*, MJL Siconelli*, QM Tran, JR Fauver, RD Carvalho, FZ Dezordi, MR Pereira, LA deCastro-Jorge, ECM Minto, LMR Passos, CC Kalinich, ME Petrone, E Allen, G España, AT Huang, DAT Cummings, G Baele, RFO Franca^, BAL da Fonseca^, TA Perkins^, GL Wallau^, ND Grubaugh^
Nature Communications 12:2619
html | pdf
Co-circulation and misdiagnosis led to underestimation of the 2015-2017 Zika epidemic in the Americas
RJ Oidtman, G España, TA Perkins
PLOS Neglected Tropical Diseases 15:e0009208
html | pdf
Air passenger travel and international surveillance data predict spatiotemporal variation in measles importations to the United States
M Poterek, MUG Kraemer, A Watts, K Khan, TA Perkins
Pathogens 10:155
html | pdf
Dynamical characteristics of Covid-19 epidemic: Estimation from Colombia's case
H Diaz, G España, N Castañeda, L Rodriguez, F de la Hoz-Restrepo
International Journal of Infectious Diseases
html | pdf
Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study
X Li, C Mukandavire, ZM Cucunubá, S Echeverria Londono, K Abbas, HE Clapham, M Jit, HL Johnson, T Papadopoulos, E Vynnycky, M Brisson, ED Carter, A Clark, MJ de Villliers, K Eilertson, MJ Ferrari, I Gamkrelidze, KAM Gaythorpe, NC Grassly, TB Hallett, W Hinsley, ML Jackson, K Jean, A Karachaliou, P Klepac, J Lessler, X Li, SM Moore, S Nayagam, DM Nguyen, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, S Sy, Y Tam, H Tanvir, QM Tran, CL Trotter, S Truelove, K van Zandvoort, S Verguet, N Walker, A Winter, K Woodruff, NM Ferguson, T Garske
Lancet 397:398-408
html | pdf
Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics
KL Schaber, TA Perkins, AL Lloyd, LA Waller, U Kitron, VA Paz-Soldan, JP Elder, AL Rothman, DJ Civitello, WH Elson, AC Morrison, TW Scott, GM Vazquez-Prokopec
PLOS Computational Biology 17:e1008627
html | pdf
2020
Hidden heterogeneity and its influence on dengue vaccination impact
MK Walters, TA Perkins
Infectious Disease Modelling 5:783
html | pdf | code
Seven challenges for spatial analyses of vector-borne diseases
TA Perkins, G España, SM Moore, RJ Oidtman, S Sharma, B Singh, AS Siraj, KJ Soda, M Smith, MK Walters, E Michael
In: Population Biology of Vector-Borne Diseases (Drake, Bonsall, Strand eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas
SM Moore, RJ Oidtman, KJ Soda, AS Siraj, RC Reiner, Jr., CM Barker, TA Perkins
PLOS Neglected Tropical Diseases 14:e0008640
html | pdf | code
Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes
QA ten Bosch, JM Wagman, F Castro-Llanos, NL Achee, JP Grieco, TA Perkins
PLOS Computational Biology 16:e1008190
html | pdf | code | data
Optimal control of the COVID-19 pandemic with non-pharmaceutical interventions
TA Perkins, G España
Bulletin of Mathematical Biology 82:118
html | pdf | code | shiny
Pre-preprint: April 21, 2020
Initial Twitter thread: April 21, 2020
Estimating unobserved SARS-CoV-2 infections in the United States
TA Perkins*, SM Cavany*, SM Moore*, RJ Oidtman, A Lerch, M Poterek
Proceedings of the National Academy of Sciences
html | pdf | code
Pre-preprint: March 15, 2020
Initial code shared: March 12, 2020
Initial Twitter thread: March 10, 2020
Theories of diversity in disease ecology
TA Perkins, JR Rohr
In: Theoretical Ecology: Concepts and Applications (McCann and Gellner, eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Malaria elimination in Costa Rica: changes in treatment and mass drug administration
LF Chaves, JH Huber, O Rojas Salas, M Ramirez Rojas, LM Romero, JM Gutierrez Alvarado, TA Perkins, M Prado, RM Rodriguez
Microorganisms 8:984
html | pdf
Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19
A Bivins, D North, A Ahmad, W Ahmed, E Alm, F Been, P Bhattacharya, L Bijlsma, AB Boehm, J Brown, G Buttiglieri, V Calabro, A Carducci, A Castiglioni, Z Gurol, S Chakraborty, F Costa, S Curcio, F de los Reyes, J Vela, K Farkas, X Fernandez-Casi, C Gerba, D Gerrity, R Girones, R Gonzalez, E Haramoto, A Harris, P Holden, M Islam, D Jones, B Kasprzyk-Hordern, M Kitajima, N Kotlarz, M Kumar, K Kuroda, G La Rosa, F Malpei, M Mautus, S McLellan, G Medema, J Meschke, J Mueller, R Newton, D Nilsson, R Noble, A van Nuijs, J Peccia, TA Perkins, A Pickering, J Rose, G Sanchez, A Smith, L Stadler, C Stauber, K Thomas, T van der Voorn, K Wigginton, K Zhu, K Bibby
Environmental Science and Technology
html | pdf
Mapping global variation in human mobility
MUG Kraemer, A Sadilek, Q Zhang, NA Marchal, G Tuli, EL Cohn, Y Hswen, TA Perkins, DL Smith, RC Reiner, JS Brownstein
Nature Human Behavior
html | pdf
Modeling human migration across spatial scales in Colombia
AS Siraj, A Sorichetta, G España, AJ Tatem, TA Perkins
PLOS ONE 15:e0232702
html | pdf
Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response
SM Cavany, G España, AL Lloyd, LA Waller, U Kitron, H Astete, WH Elson, GM Vazquez-Prokopec, TW Scott, AC Morrison, RC Reiner Jr., TA Perkins
PLOS Computational Biology 16:e1007743
html | pdf
Ecological dynamics impacting bluetongue virus transmission in North America
CE Mayo, EG McDermott, J Kopanke, M Stenglein, J Lee, C Mathiason, M Carpenter, K Reed, TA Perkins
Frontiers in Veterinary Science
html | pdf
Aggregated mobility data could help fight COVID-19
CO Buckee, S Balsari, J Chan, M Crosas, F Dominici, U Gasser, YH Grad, B Grenfell, ME Halloran, MUG Kraemer, M Lipsitch, CJE Metcalf, LA Meyers, TA Perkins, M Santillana, SV Scarpino, C Viboud, A Wesolowski, A Schroeder
Science doi:10.1126/eabb8021
html | pdf
The basic reproductive number for disease systems with multiple coupled heterogeneities
A Lloyd, U Kitron, TA Perkins, GM Vazquez-Prokopec, L Waller
Mathematical Biosciences 321:108294
html | pdf
2019
Dengue illness impacts daily human mobility patterns in Iquitos, Peru
KL Schaber, VA Paz-Soldan, AC Morrison, WHD Elson, AL Rothman, CN Mores, H Astete-Vega, TW Scott, LA Waller, U Kitron, JP Elder, CM Barker, TA Perkins, GM Vazquez-Prokopec
PLOS Neglected Tropical Diseases 13:e0007756
html | pdf | code
Pre-vaccination screening strategies for the use of the CYD-TDV dengue vaccine: a meeting report
A Wilder-Smith, PG Smith, R Luo, C Kelly-Cirino, D Curry, H Larson, A Durbin, M Chu, P Tharmaphornpilas, LC Ng, AMC Sartori, EJA Luna, DJ Gubler, G España, IK Yoon, S Flasche
Vaccine 37 5137-5146
html | pdf
Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic
N Grubaugh, S Saraf, K Gangavarapu, A Watts, AL Tan, RJ Oidtman, JT Ladner, G Oliveira, NL Matteson, MUG Kraemer, CBF Vogels, A Hentoff, D Bhatia, D Stanek, B Scott, V Landis, I Stryker, M Cone, E Kopp, A Cannons, L Heberlein-Larson, S White, L Gillis, M Ricciardi, J Kwal, P Lichtenberger, D Magnani, D Watkins, G Palacios, DH Hamer, GeoSentinel Surveillance Network, L Gardner, TA Perkins, G Baele, K Khan, A Morrison, S Isern, SF Michael, KG Andersen
Cell 178:1057-1071 doi:10.1016/j.cell.2019.07.018
html | pdf
Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data
TA Perkins*, I Rodriguez-Barraquer*, C Manore*, AS Siraj, G España, CM Barker, MA Johansson, RC Reiner, Jr.*
Epidemics 100357
html | pdf | code
Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure
G España, Y Yao, KB Anderson, MC Fitzpatrick, DL Smith, AC Morrison, A Wilder-Smith, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases 13:e0007482
html | pdf | app
Downgrading disease transmission risk estimates using terminal importations
SJ Fox, SE Bellan, TA Perkins, MA Johansson, LA Meyers
PLOS Neglected Tropical Diseases 13:e0007395
html | pdf
Estimating the impact of city-wide Aedes aegypti population control: an observational study in Iquitos, Peru
RC Reiner, Jr., S Stoddard, G Vazquez-Prokopec, H Astete, TA Perkins, M Sihuincha, J Stancil, DL Smith, T Kochel, E Halsey, U Kitron, AC Morrison, TW Scott
PLOS Neglected Tropical Diseases 13:e0007255
html | pdf
An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
TA Perkins*, RC Reiner, Jr.*, G España*, QA ten Bosch, A Verma, K Liebman, VA Paz-Soldan, JP Elder, AC Morrison, ST Stoddard, U Kitron, GM Vazquez-Prokopec, TW Scott, DL Smith
PLOS Computational Biology 15:e1006710
html | pdf | code
Inter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China
RJ Oidtman, S Lai, Z Huang, J Yang, AS Siraj, RC Reiner, Jr., AJ Tatem, TA Perkins, H Yu
Nature Communications 10:1148
html | pdf | code
Spatial sorting as the spatial analogue of natural selection
BL Phillips, TA Perkins
Theoretical Ecology 12:155-163
html | pdf
Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus
MUG Kraemer*, RC Reiner, Jr.*, OJ Brady*, JP Messina*, M Gilbert*, DM Pigott, D Yi, K Johnson, L Earl, LB Marczak, S Shirude, ND Weaver, D Bisanzio, TA Perkins, S Lai, X Lu, P Jones, GE Coelho, RG Carvalho, W Van Bortel, C Marsboom, G Hendrickx, F Schaffner, CG Moore, HH Nax, L Bengtsson, E Wetter, AJ Tatem, JS Brownstein, DL Smith, L Lambrechts, S Cauchemez, C Linard, NR Faria, OG Pybus, TW Scott, Q Liu, H Yu, GRW Wint, SI Hay, N Golding
Nature Microbiology
html | pdf
Letter to the editor in response to 'Reconstruction and prediction of viral disease epidemics'
TA Perkins
Epidemiology and Infection 147:398
html | pdf
Biased efficacy estimates in phase-III dengue vaccine trials due to heterogeneous exposure and differential detectability of primary infections across trial arms
G España, C Hogea, A Guignard, QA ten Bosch, AC Morrison, DL Smith, TW Scott, A Schmidt, TA Perkins
PLOS ONE 14:e0210041
html | pdf
Arbovirus coinfection and co-transmission: a neglected public health concern?
CBF Vogels*, C Ruckert*, SM Cavany*, TA Perkins, GD Ebel, ND Grubaugh
PLOS Biology 17:e3000130
html | pdf | code
2018
Mapping malaria by combining parasite genomic and epidemiologic data
A Wesolowski, A Taylor, H-H Chang, R Verity, S Tessema, J Bailey, TA Perkins, D Neafsey, B Greenhouse, CO Buckee
BMC Medicine 16:190
html | pdf
Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity
SM Moore, QA ten Bosch, AS Siraj, KJ Soda, G España, A Campo, S Gómez, D Salas, B Raybaud, E Wenger, P Welkhoff, TA Perkins
BMC Medicine 16:152
html | pdf | code
Exploring scenarios of chikungunya mitigation with a data-driven agent-based model of the 2014-2016 outbreak in Colombia
G España, J Grefenstette, TA Perkins, C Torres, A Campo Carey, H Diaz, F de la Hoz, DS Burke, WG van Panhuis
Scientific Reports 8:12201
html | pdf
Implementation and applications of EMOD, an individual-based multi-disease modeling platform
A Bershtyn, J Gerardin, D Bridenbecker, CW Lorton, J Bloedow, RS Baker, G Chabot-Couture, Y Chen, T Fischle, K Frey, JS Gauld, H Hu, AS Izzo, DJ Klein, D Lukacevic, KA McCarthy, JC Miller, AL Ouedraogo, TA Perkins, J Steinkraus, QA ten Bosch, HF Ting, S Titova, BG Wagner, PA Welkhoff, EA Wenger, CN Wiswell
Pathogens and Disease 76:fty059
html
Model-based analysis of experimental data from interconnected, row-configured huts elucidates multifaceted effects of a volatile chemical on Aedes aegypti mosquitoes
QA ten Bosch, F Castro-Llanos, H Manda, AC Morrison, JP Grieco, NL Achee, TA Perkins
Parasites and Vectors 11:365
html | pdf. | code
Inferences about spatiotemporal variation in dengue virus transmission are sensitive to assumptions about human mobility: a case study using geolocated tweets from Lahore, Pakistan
MUG Kraemer, D Bisanzio, RC Reiner, Jr., R Zakar, JB Hawkins, CC Freifeld, DL Smith, SI Hay, JS Brownstein, TA Perkins
EPJ Data Science 7:16
html | pdf
Contributions from the silent majority dominate dengue virus transmission
QA ten Bosch, HE Clapham, L Lambrechts, V Duoung, P Buchy, BM Althouse, AL Loyd, LA Waller, AC Morrison, U Kitron, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Pathogens 14:e1006965
html | pdf | code | data
Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia
AS Siraj, I Rodriguez-Barraquer, CM Barker, N Tejedor-Garavito, D Harding, C Lorton, D Lukacevic, G Oates, G España, MUG Kraemer, C Manore, MA Johansson, AJ Tatem, RC Reiner, Jr., TA Perkins
Scientific Data 5:180073
html | pdf
DTK-Dengue: A new agent-based model of dengue virus transmission dynamics
KJ Soda, SM Moore, G España, J Bloedow, B Raybaud, B Althouse, MA Johansson, E Wenger, P Welkhoff, TA Perkins*, QA ten Bosch*
bioRxiv doi:10.1101/376533
html | pdf
2017
Assessing the population at risk of Zika virus in Asia - is the emergency really over?
AS Siraj, TA Perkins
BMJ Global Health 2:e000309
html | pdf | code
Temperature modulates dengue virus epidemic growth rates through its effects on reproduction numbers and generation intervals
AS Siraj, RJ Oidtman, JH Huber, MUG Kraemer, OJ Brady, MA Johansson, TA Perkins
PLOS Neglected Tropical Diseases 11:e0005797
html | pdf | code
Retracing Zika's footsteps across the Americas with computational modeling
TA Perkins
Proceedings of the National Academy of Sciences 114:5558-5560
html | pdf
Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017
Zika Modeling and Projections for Vaccination Trials Collaboration (in alphabetical order): J Asher, C Barker, G Chen, D Cummings, M Chinazzi, S Daniel-Wyman, M Fischer, N Ferguson, D Follman, ME Halloran, M Johansson, K Kugeler, J Kwan, J Lessler, IM Longini, S Merler, A Monaghan, A Pastore y Piontti, TA Perkins, DR Prevots, RC Reiner, Jr., L Rossi, I Rodriguez-Barraquer, AS Siraj, K Sun, A Vespignanni, Q Zhang
bioRxiv doi:10.1101/187591
html | pdf
2016
The long-term safety, public health impact, and cost-effectiveness of routine vaccination with a recombinant, live-attenuated dengue vaccine (Dengvaxia): A model comparison study
S Flasche*, M Jit*, I Rodriguez-Barraquer*, L Coudeville*, M Recker*, K Koelle*, G Milne*, TJ Hladish*, TA Perkins*, DAT Cummings, I Dorigatti, DJ Laydon, G España, J Kelso, I Longini, J Lourenco, CAB Pearson, RC Reiner, Jr., L Mier-y-Teran-Romero, K Vannice, N Ferguson
PLOS Medicine 13:e1002181
html | pdf | commentary
Pokemon Go and exposure to mosquito-borne diseases: How not to catch 'em all
RJ Oidtman, RC Christofferson, QA ten Bosch, G España, MUG Kraemer, AJ Tatem, CM Barker, TA Perkins
PLOS Currents Outbreaks
html
Quantitative, model-based estimates of variability in the generation and serial intervals of Plasmodium falciparum malaria
JH Huber, GL Johnston, B Greenhouse, DL Smith, TA Perkins
Malaria Journal 15:490
html | pdf | code
After the games are over: life-history trade-offs drive dispersal attenuation following range expansion
TA Perkins, C Boettiger, BL Phillips
Ecology and Evolution doi:10.1002/ece3.2314
html | pdf | code
Model-based projections of Zika virus infections in childbearing women in the Americas
TA Perkins, AS Siraj, C Warren Ruktanonchai, MUG Kraemer, AJ Tatem
Nature Microbiology 1:16126
html | pdf | code
Calling in sick: impacts of fever on intra-urban human mobility
TA Perkins, VA Paz Soldan, ST Stoddard, AC Morrison, BM Forshey, KC Long, ES Halsey, TJ Kochel, JP Elder, U Kitron, TW Scott, GM Vazquez-Prokopec
Proceedings of the Royal Society B 283:20160390
html | pdf | code | data
Quantifying the epidemiological impact of vector control on dengue
RC Reiner, Jr., N Achee, R Barrera, TR Burkot, DD Chadee, G Devine, T Endy, D Gubler, J Homback, I Kleinschmidt, A Lenhart, S Lindsay, I Longini, M Mondy, AC Morrison, TA Perkins, GM Vazquez-Prokopec, P Reiter, S Ritchie, DL Smith, D Strickman, TW Scott
PLOS Neglected Tropical Diseases 10:e0004588
html | pdf
Coupled heterogeneities and their impact on parasite transmission and control
GM Vazquez-Prokopeck, TA Perkins, LA Waller, AL Lloyd, RC Reiner, Jr., TW Scott, U Kitron
Trends in Parasitology 32:356-367
html | pdf
Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, ME Sinka, CL Moyes, PA Eckhoff, TW Scott, SW Lindsay, SI Hay, DL Smith
Transactions of the Royal Society of Tropical Medicine and Hygiene 110:107-117
html | pdf
2015
Mapping residual transmission for malaria elimination
RC Reiner, Jr., A Le Menach, S Kunene, N Ntshalintshali, M Hsiang, TA Perkins, B Greenhouse, AJ Tatem, JM Cohen, DL Smith
eLife 4:e09520
html | pdf
Big city, small world: density, contact rates, and transmission of dengue across Pakistan
MUG Kraemer, TA Perkins, DAT Cummings, R Zakar, SI Hay, DL Smith, RC Reiner, Jr.
Journal of the Royal Society Interface 12:20150468
html | pdf
A critical assessment of vector control for dengue prevention
NL Achee, F Gould, TA Perkins, RC Reiner, Jr., AC Morrison, SA Ritchie, DJ Gubler, R Teyssou, TW Scott
PLOS Neglected Tropical Diseases 9:e0003655
html | pdf
The changing epidemiology of dengue in China, 1990-2014: a descriptive analysis of 25 years of nationwide surveillance data
S Lai, Z Huang, H Zhou, KL Anders, TA Perkins, W Yin, Y Li, D Mu, Q Chen, Z Zhang, Y Qiu, L Wang, H Zhang, L Zeng, X Ren, M Geng, Z Li, AJ Tatem, SI Hay, H Yu
BMC Medicine 13:100
html | pdf | commentary
Adult vector control, mosquito ecology, and malaria transmission
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, TW Scott, SW Lindsay, SI Hay, DL Smith
International Health 7:121-129
html | pdf
Estimating drivers of autochthonous transmission of chikungunya virus in its invasion of the Americas
TA Perkins, CJE Metcalf, BT Grenfell, AJ Tatem
PLOS Currents Outbreaks
html | code
2014 and before
See Alex's Google Scholar page for a list of his publications prior to forming his lab at Notre Dame.
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges
SM Cavany, C Barbera, M Carpenter, C Rodgers, M Stenglein, C Mayo, TA Perkins
bioRxiv doi:10.1101/2022.06.03.494504
html | pdf
Expected endpoints from future chikungunya vaccine trial sites informed by serological data and modeling
QM Tran, KJ Soda, AS Siraj, SM Moore, HE Clapham, TA Perkins
medRxiv doi:10.1101/2022.05.23.22275466
html | pdf | code
Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
ML Poterek, CBF Vogels, ND Grubaugh, GD Ebel, TA Perkins, SM Cavany
medRxiv doi:10.1101/2022.05.05.22274743
html | pdf
An epidemiological and intervention assessment of the malaria epidemic in Bolivar, Venezuela: a modelling study
JH Huber, LF Chaves, AS Siraj, JE Moreno, ME Guevara, M Villegas, L Pocaterra, L Villegas, TA Perkins
medRxiv doi:10.1101/2022.04.19.22274042
html | pdf
Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study
RK Borchering, LC Mulllany, E Howerton, M Chinazzi, CP Smith, M Qin, NG Reich, L Contamin, J Levander, J Kerr, J Espino, H Hochheiser, K Lovett, M Kinsey, K Tallaksen, S Wilson, L Shin, JC Lemaitre, JD Hulse, J Kaminsky, EC Lee, JT Davis, K Mu, X Xiong, A Pastore y Piontti, A Vespignani, A Srivastava, P Porebski, S Venkatramanan, A Adiga, B Lewis, B Klahn, J Outten, B Hurt, J Chen, H Mortveit, A Wilson, M Marathe, S Hoops, P Bhattacharya, D Machi, S Chen, R Paul, D Janies, JC Thill, M Galanti, T Yamana, S Pei, J Shaman, G España, S Cavany, S Moore, TA Perkins, JM Healy, RB Slayton, MA Johansson, M Biggerstaff, K Shea, SA Truelove, MC Runge, C Viboud, J Lessler
medRxiv doi:10.1101/2022.03.08.22271905
html | pdf
Prioritizing interventions for preventing COVID-19 outbreaks in military basic training
G España*, TA Perkins*, S Pollett, ME Smith, SM Moore, PO Kwon, TL Hall, MH Beagle Jr., CK Murray, S Hakre, S Peel, K Modjarrad, PT Scott
medRxiv doi:10.1101/2021.11.28.21266969
html | pdf | code
Ignoring transmission dynamics leads to underestimation of the impact of a novel intervention against mosquito-borne disease
SM Cavany*, JH Huber*, A Wieler, M Elliott, QM Tran, G España, SM Moore, TA Perkins
medRxiv doi:10.1101/2021.11.19.21266602
html | pdf
Misdiagnosis prevents accurate monitoring of transmission and burden for sub-critical pathogens: a case study of Plasmodium knowlesi malaria
JH Huber
medRxiv doi:10.1101/2021.09.13.21263501
html | pdf
The potential impact of delta variant of SARS-CoV-2 in the context of limited vaccination coverage and increasing social mixing in Bogotá, Colombia
G España, ZM Cucunubá, J Cuervo-Rojas, H Díaz, M González-Mayorga, JD Ramírez
medRxiv doi:10.1101/2021.08.06.21261734
html | pdf
COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support
K Shea, RK Borchering, WJM Probert, E Howerton, TL Bogich, S Li, WG van Panhuis, C Viboud, R Aguas, A Belov, SH Bhargava, S Cavany, JC Chang, C Chen, J Chen, S Chen, YQ Chen, LM Childs, CC Chow, I Crooker, SY Del Valle, G España, G Fairchild, RC Gerkin, TC Germann, Q Gu, X Guan, L Guo, GR Hart, TJ Hladish, N Hupert, D Janies, CC Kerr, DJ Klein, E Klein, G Lin, C Manore, LA Meyers, J Mittler, K Mu, RC Nunez, R Oidtman, R Pasco, A Pastore y Pionti, R Paul, CAB Pearson, D Perdomo, TA Perkins, K Pierce, AN Pillai, RC Rael, K Rosenfeld, CW Ross, JA Spencer, AB Stoltzfus, KB Toh, S Vattikuti, A Vespignani, L Wang, L White, P Xu, Y Yang, ON Yogurtcu, W Zhang, Y Zhao, D Zou, M Ferrari, D Pannell, M Tildesley, J Seifarth, E Johnson, M Biggerstaff, M Johansson, RB Slayton, J Levander, J Stazer, J Salermo, MC Runge
medRxiv doi:10.1101/2020.11.03.20225409
html | pdf
Ensemble forecasts of coronavirus disease 2019 (COVID-19) in the U.S.
EL Ray, N Wattanachit, J Niemi, AH Kanji, K House, EY Cramer, J Bracher, Andrew Zheng, TK Yamana, X Xiong, S Woody, Y Wang, L Wang, RL Walraven, V Tomar, K Sherratt, D Sheldon, RC Reiner, BA Prakash, D Osthus, ML Li, EC Lee, U Koyluoglu, P Keskinocak, Y Gu, Q Gu, GE George, G España, S Corsetti, J Chhatwal, S Cavany, H Biegel, M Ben-Nun, J Walker, R Slayton, V Lopez, M Biggerstaff, MA Johansson, NG Reich, COVID-19 Forecast Hub Consortium
medRxiv doi:10.1101/2020.08.19.20177493
html | pdf
2022
The impact of emerging Plasodium knowlesi on accurate diagnosis by light microscopy: a systematic review and modeling analysis
JH Huber, M Elliott, C Koepfli, TA Perkins
In press at American Journal of Tropical Medicine and Hygiene
html | pdf
Designing school reopening in the COVID-19 pre-vaccination period in Bogotá, Colombia: A modeling study
G España*, Z Cucunubá*, H Diaz, S Cavany, N Castañeda, L Rodriguez
PLOS Global Public Health 2:e0000467
html | pdf
Projecting vaccine demand and impact for emerging zoonotic pathogens
A Lerch, QA ten Bosch, M L'Azou-Jackson, AA Bettis, M Bernuzzi, GAV Murphy, QM Tran, JH Huber, A Siraj, M Elliott, C Hartlage, K Koh, K Strimbu, M Walters, TA Perkins, SM Moore
BMC Medicine
html | pdf | code | app
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States
EY Cramer, EL Ray, VK Lopez, ... , 284 authors including S Cavany, G España, S Moore, R Oidtman, TA Perkins, ... , RB Slayton, MA Johansson, M Biggerstaff, NG Reich
Proceedings of the National Academy of Sciences 119:e2113561119
html | pdf
Inferring person-to-person networks of pathogen transmission: is routine surveillance data up to the task?
JH Huber, MS Hsiang, N Dlamini, M Murphy, S Vilakati, N Nhlabathi, A Lerch, R Nielsen, N Ntshalintshali, B Greenhouse, TA Perkins
Malaria Journal 21:58
html | pdf
Bluetongue research at a crossroads: modern genomics tools can pave the way to new insights
J Kopanke, M Carpenter, J Lee, K Reed, C Rodgers, M Burton, K Lovett, JA Westrich, E McNulty, E McDermott, C Barbera, S Cavany, JR Rohr, TA Perkins, CK Mathiason, M Stenglein, C Mayo
Annual Review of Animal Biosciences 10:303
html | pdf
Performance of three molecular tests for SARS-CoV-2 on a university campus estimated jointly with Bayesian latent class modeling
TA Perkins, M Stephens, W Alvarez Barrios, SM Cavany, L Rulli, ME Pfrender
Microbiology Spectrum
html | pdf | code
Inferring SARS-CoV-2 RNA shedding into wastewater relative to time of infection
SM Cavany, A Bivins, Z Wu, D North, K Bibby*, TA Perkins*
Epidemiology and Infection
html | pdf
2021
Site-specific biases in phase-III clinical trials underestimate the effect of radical cure against Plasmodium vivax hypnozoites
JH Huber, C Koepfli, G España, N Nekkab, MT White, TA Perkins
Malaria Journal
html | pdf
Timing is everything when it comes to pertussis vaccination
TA Perkins, QM Tran
Lancet Infectious Diseases
html
The current burden of Japanese encephalitis and the estimated impacts of vaccination: Combining estimates of the spatial distribution and transmission intensity of a zoonotic pathogen
SM Moore
PLOS Neglected Tropical Diseases 15:e0009385
html | pdf | code
Burden is in the eye of the beholder: sensitivity of yellow fever disease burden estimates to modeling assumptions
TA Perkins, JH Huber, QM Tran, RJ Oidtman, MK Walters, AS Siraj, SM Moore
Science Advances 7:eabg5033
html | pdf | code
Trade-offs between individual and ensemble forecasts of an emerging infectious disease
RJ Oidtman, E Omodei, MUG Kraemer, CA Castaneda-Orjuela, E Cruz-Rivera, S Misnaza-Castrillon, MP Cifuentes, LE Rincon, V Canon, P de Alarcon, G España, JH Huber, SC Hill, CM Barker, MA Johansson, CA Manore, RC Reiner, I Rodriguez-Barraquer, AS Siraj, E Frias-Martinez, M Garcia-Herranz, TA Perkins
Nature Communications 12:5379
html | pdf
Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA
G España, SM Cavany*, RJ Oidtman*, C Barbera, A Costello, A Lerch, M Poterek, Q Tran, A Wieler, S Moore, TA Perkins
Epidemics 37:100487
html | pdf
Pre-preprint: August 21, 2020
Initial Twitter thread: August 21, 2020
Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world
J Toor, S Echeverria-Londono, X Li, K Abbas, ED Carter, HE Clapham, A Clark, MJ de Villiers, K Eilertson, M Ferrari, I Gamkrelidze, TB Hallett, WR Hinsley, D Hogan, JH Huber, ML Jackson, K Jean, M Jit, A Karachaliou, P Klepac, A Kraay, J Lessler, X Li, BA Lopman, T Mengistu, CJE Metcalf, SM Moore, S Nayagam, T Papadopoulos, TA Perkins, A Portnoy, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, Y Tam, H Tanvir, QM Tran, CL Trotter, SA Truelove, E Vynnycky, N Walker, A Winter, K Woodruff, NM Ferguson, KAM Gaythorpe
eLife 10:e67635
html | pdf
The impact of dengue illness on social distancing and caregiving behavior
KL Schaber, AC Morrison, WH Elson, H Astete-Vega, JJ Córdova-López, EJ Ríos López, WL Quiroz Flores, AS Vizcarra Santillan, TW Scott, LA Waller, U Kitron, CM Barker, TA Perkins, AL Rothman, G Vazquez-Prokopec, JP Elder
PLOS Neglected Tropical Diseases
html | pdf
Cost-effectiveness of dengue vaccination in Puerto Rico
G España, AJ Leidner, S Waterman, TA Perkins
PLOS Neglected Tropical Diseases
html | pdf
Pandemic-associated mobility restrictions could cause increases in dengue virus transmission
SM Cavany, G España, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases
html | pdf
Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries
K Gaythorpe*, K Abbas*, JH Huber*, A Karachaliou*, N Thakkar*, K Woodruff, X Li, S Echeverria-Londono, VIMC Working Group on COVID-19 Impact on Vaccine Preventable Disease, M Ferrari^, ML Jackson^, K McCarthy^, TA Perkins^, C Trotter^, M Jit^
eLife 10:e67023
html | pdf
Over 100 years of Rift Valley fever: a patchwork of data on pathogen spread and spillover
GM Bron, K Strimbu, H Cecilia, A Lerch, SM Moore, Q Tran, TA Perkins, QA ten Bosch
Pathogens 10:708
html | pdf
Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
AF Brito*, LC Machado*, RJ Oidtman*, MJL Siconelli*, QM Tran, JR Fauver, RD Carvalho, FZ Dezordi, MR Pereira, LA deCastro-Jorge, ECM Minto, LMR Passos, CC Kalinich, ME Petrone, E Allen, G España, AT Huang, DAT Cummings, G Baele, RFO Franca^, BAL da Fonseca^, TA Perkins^, GL Wallau^, ND Grubaugh^
Nature Communications 12:2619
html | pdf
Co-circulation and misdiagnosis led to underestimation of the 2015-2017 Zika epidemic in the Americas
RJ Oidtman, G España, TA Perkins
PLOS Neglected Tropical Diseases 15:e0009208
html | pdf
Air passenger travel and international surveillance data predict spatiotemporal variation in measles importations to the United States
M Poterek, MUG Kraemer, A Watts, K Khan, TA Perkins
Pathogens 10:155
html | pdf
Dynamical characteristics of Covid-19 epidemic: Estimation from Colombia's case
H Diaz, G España, N Castañeda, L Rodriguez, F de la Hoz-Restrepo
International Journal of Infectious Diseases
html | pdf
Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study
X Li, C Mukandavire, ZM Cucunubá, S Echeverria Londono, K Abbas, HE Clapham, M Jit, HL Johnson, T Papadopoulos, E Vynnycky, M Brisson, ED Carter, A Clark, MJ de Villliers, K Eilertson, MJ Ferrari, I Gamkrelidze, KAM Gaythorpe, NC Grassly, TB Hallett, W Hinsley, ML Jackson, K Jean, A Karachaliou, P Klepac, J Lessler, X Li, SM Moore, S Nayagam, DM Nguyen, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, S Sy, Y Tam, H Tanvir, QM Tran, CL Trotter, S Truelove, K van Zandvoort, S Verguet, N Walker, A Winter, K Woodruff, NM Ferguson, T Garske
Lancet 397:398-408
html | pdf
Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics
KL Schaber, TA Perkins, AL Lloyd, LA Waller, U Kitron, VA Paz-Soldan, JP Elder, AL Rothman, DJ Civitello, WH Elson, AC Morrison, TW Scott, GM Vazquez-Prokopec
PLOS Computational Biology 17:e1008627
html | pdf
2020
Hidden heterogeneity and its influence on dengue vaccination impact
MK Walters, TA Perkins
Infectious Disease Modelling 5:783
html | pdf | code
Seven challenges for spatial analyses of vector-borne diseases
TA Perkins, G España, SM Moore, RJ Oidtman, S Sharma, B Singh, AS Siraj, KJ Soda, M Smith, MK Walters, E Michael
In: Population Biology of Vector-Borne Diseases (Drake, Bonsall, Strand eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas
SM Moore, RJ Oidtman, KJ Soda, AS Siraj, RC Reiner, Jr., CM Barker, TA Perkins
PLOS Neglected Tropical Diseases 14:e0008640
html | pdf | code
Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes
QA ten Bosch, JM Wagman, F Castro-Llanos, NL Achee, JP Grieco, TA Perkins
PLOS Computational Biology 16:e1008190
html | pdf | code | data
Optimal control of the COVID-19 pandemic with non-pharmaceutical interventions
TA Perkins, G España
Bulletin of Mathematical Biology 82:118
html | pdf | code | shiny
Pre-preprint: April 21, 2020
Initial Twitter thread: April 21, 2020
Estimating unobserved SARS-CoV-2 infections in the United States
TA Perkins*, SM Cavany*, SM Moore*, RJ Oidtman, A Lerch, M Poterek
Proceedings of the National Academy of Sciences
html | pdf | code
Pre-preprint: March 15, 2020
Initial code shared: March 12, 2020
Initial Twitter thread: March 10, 2020
Theories of diversity in disease ecology
TA Perkins, JR Rohr
In: Theoretical Ecology: Concepts and Applications (McCann and Gellner, eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Malaria elimination in Costa Rica: changes in treatment and mass drug administration
LF Chaves, JH Huber, O Rojas Salas, M Ramirez Rojas, LM Romero, JM Gutierrez Alvarado, TA Perkins, M Prado, RM Rodriguez
Microorganisms 8:984
html | pdf
Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19
A Bivins, D North, A Ahmad, W Ahmed, E Alm, F Been, P Bhattacharya, L Bijlsma, AB Boehm, J Brown, G Buttiglieri, V Calabro, A Carducci, A Castiglioni, Z Gurol, S Chakraborty, F Costa, S Curcio, F de los Reyes, J Vela, K Farkas, X Fernandez-Casi, C Gerba, D Gerrity, R Girones, R Gonzalez, E Haramoto, A Harris, P Holden, M Islam, D Jones, B Kasprzyk-Hordern, M Kitajima, N Kotlarz, M Kumar, K Kuroda, G La Rosa, F Malpei, M Mautus, S McLellan, G Medema, J Meschke, J Mueller, R Newton, D Nilsson, R Noble, A van Nuijs, J Peccia, TA Perkins, A Pickering, J Rose, G Sanchez, A Smith, L Stadler, C Stauber, K Thomas, T van der Voorn, K Wigginton, K Zhu, K Bibby
Environmental Science and Technology
html | pdf
Mapping global variation in human mobility
MUG Kraemer, A Sadilek, Q Zhang, NA Marchal, G Tuli, EL Cohn, Y Hswen, TA Perkins, DL Smith, RC Reiner, JS Brownstein
Nature Human Behavior
html | pdf
Modeling human migration across spatial scales in Colombia
AS Siraj, A Sorichetta, G España, AJ Tatem, TA Perkins
PLOS ONE 15:e0232702
html | pdf
Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response
SM Cavany, G España, AL Lloyd, LA Waller, U Kitron, H Astete, WH Elson, GM Vazquez-Prokopec, TW Scott, AC Morrison, RC Reiner Jr., TA Perkins
PLOS Computational Biology 16:e1007743
html | pdf
Ecological dynamics impacting bluetongue virus transmission in North America
CE Mayo, EG McDermott, J Kopanke, M Stenglein, J Lee, C Mathiason, M Carpenter, K Reed, TA Perkins
Frontiers in Veterinary Science
html | pdf
Aggregated mobility data could help fight COVID-19
CO Buckee, S Balsari, J Chan, M Crosas, F Dominici, U Gasser, YH Grad, B Grenfell, ME Halloran, MUG Kraemer, M Lipsitch, CJE Metcalf, LA Meyers, TA Perkins, M Santillana, SV Scarpino, C Viboud, A Wesolowski, A Schroeder
Science doi:10.1126/eabb8021
html | pdf
The basic reproductive number for disease systems with multiple coupled heterogeneities
A Lloyd, U Kitron, TA Perkins, GM Vazquez-Prokopec, L Waller
Mathematical Biosciences 321:108294
html | pdf
2019
Dengue illness impacts daily human mobility patterns in Iquitos, Peru
KL Schaber, VA Paz-Soldan, AC Morrison, WHD Elson, AL Rothman, CN Mores, H Astete-Vega, TW Scott, LA Waller, U Kitron, JP Elder, CM Barker, TA Perkins, GM Vazquez-Prokopec
PLOS Neglected Tropical Diseases 13:e0007756
html | pdf | code
Pre-vaccination screening strategies for the use of the CYD-TDV dengue vaccine: a meeting report
A Wilder-Smith, PG Smith, R Luo, C Kelly-Cirino, D Curry, H Larson, A Durbin, M Chu, P Tharmaphornpilas, LC Ng, AMC Sartori, EJA Luna, DJ Gubler, G España, IK Yoon, S Flasche
Vaccine 37 5137-5146
html | pdf
Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic
N Grubaugh, S Saraf, K Gangavarapu, A Watts, AL Tan, RJ Oidtman, JT Ladner, G Oliveira, NL Matteson, MUG Kraemer, CBF Vogels, A Hentoff, D Bhatia, D Stanek, B Scott, V Landis, I Stryker, M Cone, E Kopp, A Cannons, L Heberlein-Larson, S White, L Gillis, M Ricciardi, J Kwal, P Lichtenberger, D Magnani, D Watkins, G Palacios, DH Hamer, GeoSentinel Surveillance Network, L Gardner, TA Perkins, G Baele, K Khan, A Morrison, S Isern, SF Michael, KG Andersen
Cell 178:1057-1071 doi:10.1016/j.cell.2019.07.018
html | pdf
Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data
TA Perkins*, I Rodriguez-Barraquer*, C Manore*, AS Siraj, G España, CM Barker, MA Johansson, RC Reiner, Jr.*
Epidemics 100357
html | pdf | code
Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure
G España, Y Yao, KB Anderson, MC Fitzpatrick, DL Smith, AC Morrison, A Wilder-Smith, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases 13:e0007482
html | pdf | app
Downgrading disease transmission risk estimates using terminal importations
SJ Fox, SE Bellan, TA Perkins, MA Johansson, LA Meyers
PLOS Neglected Tropical Diseases 13:e0007395
html | pdf
Estimating the impact of city-wide Aedes aegypti population control: an observational study in Iquitos, Peru
RC Reiner, Jr., S Stoddard, G Vazquez-Prokopec, H Astete, TA Perkins, M Sihuincha, J Stancil, DL Smith, T Kochel, E Halsey, U Kitron, AC Morrison, TW Scott
PLOS Neglected Tropical Diseases 13:e0007255
html | pdf
An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
TA Perkins*, RC Reiner, Jr.*, G España*, QA ten Bosch, A Verma, K Liebman, VA Paz-Soldan, JP Elder, AC Morrison, ST Stoddard, U Kitron, GM Vazquez-Prokopec, TW Scott, DL Smith
PLOS Computational Biology 15:e1006710
html | pdf | code
Inter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China
RJ Oidtman, S Lai, Z Huang, J Yang, AS Siraj, RC Reiner, Jr., AJ Tatem, TA Perkins, H Yu
Nature Communications 10:1148
html | pdf | code
Spatial sorting as the spatial analogue of natural selection
BL Phillips, TA Perkins
Theoretical Ecology 12:155-163
html | pdf
Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus
MUG Kraemer*, RC Reiner, Jr.*, OJ Brady*, JP Messina*, M Gilbert*, DM Pigott, D Yi, K Johnson, L Earl, LB Marczak, S Shirude, ND Weaver, D Bisanzio, TA Perkins, S Lai, X Lu, P Jones, GE Coelho, RG Carvalho, W Van Bortel, C Marsboom, G Hendrickx, F Schaffner, CG Moore, HH Nax, L Bengtsson, E Wetter, AJ Tatem, JS Brownstein, DL Smith, L Lambrechts, S Cauchemez, C Linard, NR Faria, OG Pybus, TW Scott, Q Liu, H Yu, GRW Wint, SI Hay, N Golding
Nature Microbiology
html | pdf
Letter to the editor in response to 'Reconstruction and prediction of viral disease epidemics'
TA Perkins
Epidemiology and Infection 147:398
html | pdf
Biased efficacy estimates in phase-III dengue vaccine trials due to heterogeneous exposure and differential detectability of primary infections across trial arms
G España, C Hogea, A Guignard, QA ten Bosch, AC Morrison, DL Smith, TW Scott, A Schmidt, TA Perkins
PLOS ONE 14:e0210041
html | pdf
Arbovirus coinfection and co-transmission: a neglected public health concern?
CBF Vogels*, C Ruckert*, SM Cavany*, TA Perkins, GD Ebel, ND Grubaugh
PLOS Biology 17:e3000130
html | pdf | code
2018
Mapping malaria by combining parasite genomic and epidemiologic data
A Wesolowski, A Taylor, H-H Chang, R Verity, S Tessema, J Bailey, TA Perkins, D Neafsey, B Greenhouse, CO Buckee
BMC Medicine 16:190
html | pdf
Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity
SM Moore, QA ten Bosch, AS Siraj, KJ Soda, G España, A Campo, S Gómez, D Salas, B Raybaud, E Wenger, P Welkhoff, TA Perkins
BMC Medicine 16:152
html | pdf | code
Exploring scenarios of chikungunya mitigation with a data-driven agent-based model of the 2014-2016 outbreak in Colombia
G España, J Grefenstette, TA Perkins, C Torres, A Campo Carey, H Diaz, F de la Hoz, DS Burke, WG van Panhuis
Scientific Reports 8:12201
html | pdf
Implementation and applications of EMOD, an individual-based multi-disease modeling platform
A Bershtyn, J Gerardin, D Bridenbecker, CW Lorton, J Bloedow, RS Baker, G Chabot-Couture, Y Chen, T Fischle, K Frey, JS Gauld, H Hu, AS Izzo, DJ Klein, D Lukacevic, KA McCarthy, JC Miller, AL Ouedraogo, TA Perkins, J Steinkraus, QA ten Bosch, HF Ting, S Titova, BG Wagner, PA Welkhoff, EA Wenger, CN Wiswell
Pathogens and Disease 76:fty059
html
Model-based analysis of experimental data from interconnected, row-configured huts elucidates multifaceted effects of a volatile chemical on Aedes aegypti mosquitoes
QA ten Bosch, F Castro-Llanos, H Manda, AC Morrison, JP Grieco, NL Achee, TA Perkins
Parasites and Vectors 11:365
html | pdf. | code
Inferences about spatiotemporal variation in dengue virus transmission are sensitive to assumptions about human mobility: a case study using geolocated tweets from Lahore, Pakistan
MUG Kraemer, D Bisanzio, RC Reiner, Jr., R Zakar, JB Hawkins, CC Freifeld, DL Smith, SI Hay, JS Brownstein, TA Perkins
EPJ Data Science 7:16
html | pdf
Contributions from the silent majority dominate dengue virus transmission
QA ten Bosch, HE Clapham, L Lambrechts, V Duoung, P Buchy, BM Althouse, AL Loyd, LA Waller, AC Morrison, U Kitron, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Pathogens 14:e1006965
html | pdf | code | data
Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia
AS Siraj, I Rodriguez-Barraquer, CM Barker, N Tejedor-Garavito, D Harding, C Lorton, D Lukacevic, G Oates, G España, MUG Kraemer, C Manore, MA Johansson, AJ Tatem, RC Reiner, Jr., TA Perkins
Scientific Data 5:180073
html | pdf
DTK-Dengue: A new agent-based model of dengue virus transmission dynamics
KJ Soda, SM Moore, G España, J Bloedow, B Raybaud, B Althouse, MA Johansson, E Wenger, P Welkhoff, TA Perkins*, QA ten Bosch*
bioRxiv doi:10.1101/376533
html | pdf
2017
Assessing the population at risk of Zika virus in Asia - is the emergency really over?
AS Siraj, TA Perkins
BMJ Global Health 2:e000309
html | pdf | code
Temperature modulates dengue virus epidemic growth rates through its effects on reproduction numbers and generation intervals
AS Siraj, RJ Oidtman, JH Huber, MUG Kraemer, OJ Brady, MA Johansson, TA Perkins
PLOS Neglected Tropical Diseases 11:e0005797
html | pdf | code
Retracing Zika's footsteps across the Americas with computational modeling
TA Perkins
Proceedings of the National Academy of Sciences 114:5558-5560
html | pdf
Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017
Zika Modeling and Projections for Vaccination Trials Collaboration (in alphabetical order): J Asher, C Barker, G Chen, D Cummings, M Chinazzi, S Daniel-Wyman, M Fischer, N Ferguson, D Follman, ME Halloran, M Johansson, K Kugeler, J Kwan, J Lessler, IM Longini, S Merler, A Monaghan, A Pastore y Piontti, TA Perkins, DR Prevots, RC Reiner, Jr., L Rossi, I Rodriguez-Barraquer, AS Siraj, K Sun, A Vespignanni, Q Zhang
bioRxiv doi:10.1101/187591
html | pdf
2016
The long-term safety, public health impact, and cost-effectiveness of routine vaccination with a recombinant, live-attenuated dengue vaccine (Dengvaxia): A model comparison study
S Flasche*, M Jit*, I Rodriguez-Barraquer*, L Coudeville*, M Recker*, K Koelle*, G Milne*, TJ Hladish*, TA Perkins*, DAT Cummings, I Dorigatti, DJ Laydon, G España, J Kelso, I Longini, J Lourenco, CAB Pearson, RC Reiner, Jr., L Mier-y-Teran-Romero, K Vannice, N Ferguson
PLOS Medicine 13:e1002181
html | pdf | commentary
Pokemon Go and exposure to mosquito-borne diseases: How not to catch 'em all
RJ Oidtman, RC Christofferson, QA ten Bosch, G España, MUG Kraemer, AJ Tatem, CM Barker, TA Perkins
PLOS Currents Outbreaks
html
Quantitative, model-based estimates of variability in the generation and serial intervals of Plasmodium falciparum malaria
JH Huber, GL Johnston, B Greenhouse, DL Smith, TA Perkins
Malaria Journal 15:490
html | pdf | code
After the games are over: life-history trade-offs drive dispersal attenuation following range expansion
TA Perkins, C Boettiger, BL Phillips
Ecology and Evolution doi:10.1002/ece3.2314
html | pdf | code
Model-based projections of Zika virus infections in childbearing women in the Americas
TA Perkins, AS Siraj, C Warren Ruktanonchai, MUG Kraemer, AJ Tatem
Nature Microbiology 1:16126
html | pdf | code
Calling in sick: impacts of fever on intra-urban human mobility
TA Perkins, VA Paz Soldan, ST Stoddard, AC Morrison, BM Forshey, KC Long, ES Halsey, TJ Kochel, JP Elder, U Kitron, TW Scott, GM Vazquez-Prokopec
Proceedings of the Royal Society B 283:20160390
html | pdf | code | data
Quantifying the epidemiological impact of vector control on dengue
RC Reiner, Jr., N Achee, R Barrera, TR Burkot, DD Chadee, G Devine, T Endy, D Gubler, J Homback, I Kleinschmidt, A Lenhart, S Lindsay, I Longini, M Mondy, AC Morrison, TA Perkins, GM Vazquez-Prokopec, P Reiter, S Ritchie, DL Smith, D Strickman, TW Scott
PLOS Neglected Tropical Diseases 10:e0004588
html | pdf
Coupled heterogeneities and their impact on parasite transmission and control
GM Vazquez-Prokopeck, TA Perkins, LA Waller, AL Lloyd, RC Reiner, Jr., TW Scott, U Kitron
Trends in Parasitology 32:356-367
html | pdf
Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, ME Sinka, CL Moyes, PA Eckhoff, TW Scott, SW Lindsay, SI Hay, DL Smith
Transactions of the Royal Society of Tropical Medicine and Hygiene 110:107-117
html | pdf
2015
Mapping residual transmission for malaria elimination
RC Reiner, Jr., A Le Menach, S Kunene, N Ntshalintshali, M Hsiang, TA Perkins, B Greenhouse, AJ Tatem, JM Cohen, DL Smith
eLife 4:e09520
html | pdf
Big city, small world: density, contact rates, and transmission of dengue across Pakistan
MUG Kraemer, TA Perkins, DAT Cummings, R Zakar, SI Hay, DL Smith, RC Reiner, Jr.
Journal of the Royal Society Interface 12:20150468
html | pdf
A critical assessment of vector control for dengue prevention
NL Achee, F Gould, TA Perkins, RC Reiner, Jr., AC Morrison, SA Ritchie, DJ Gubler, R Teyssou, TW Scott
PLOS Neglected Tropical Diseases 9:e0003655
html | pdf
The changing epidemiology of dengue in China, 1990-2014: a descriptive analysis of 25 years of nationwide surveillance data
S Lai, Z Huang, H Zhou, KL Anders, TA Perkins, W Yin, Y Li, D Mu, Q Chen, Z Zhang, Y Qiu, L Wang, H Zhang, L Zeng, X Ren, M Geng, Z Li, AJ Tatem, SI Hay, H Yu
BMC Medicine 13:100
html | pdf | commentary
Adult vector control, mosquito ecology, and malaria transmission
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, TW Scott, SW Lindsay, SI Hay, DL Smith
International Health 7:121-129
html | pdf
Estimating drivers of autochthonous transmission of chikungunya virus in its invasion of the Americas
TA Perkins, CJE Metcalf, BT Grenfell, AJ Tatem
PLOS Currents Outbreaks
html | code
2014 and before
See Alex's Google Scholar page for a list of his publications prior to forming his lab at Notre Dame.
